The Runaway Swan
by captainswanaholic
Summary: CS AU: Emma Swan is a Captain in the Royal Navy, and Killian is a prince and the son of Snow and Charming.
1. Chapter 1

**The Runaway Swan**

**Chapter 1**

_Author's note: Captain Swan AU where Emma is a naval officer and Killian is prince and son of Snow and Charming._

He knew that one day this habit would get him into trouble. He had no idea it would be like this.

Every Friday at midnight, Prince Killian climbs out his window and rides into town disguised as a commoner. He always stopped at the same tavern, had a few drinks, played a few games, and snuck back to the castle before the servants woke up. It was always the same, and everyone there knew him by his alias, Liam.

One day when he arrives, he is surrounded by a completely different crowd. He swore quietly when he realized it was the crew of the Royal Navy's prize ship. He knew them, and they knew him. He pulled his hood up tighter around his head and tried to duck back out, when he bumps into a naval officer with short blond hair and piercing green eyes.

"My apologies Captain." he muttered, weaving around the officer to leave. "Why such a hasty exit, sir? Did my men offend you?" the officer asked, in a slightly higher voice than Killian expected.

"No, I just realized I have elsewhere to be, but I appreciate the concern, captain."

"I recognize that voice. You are the King's son aren't you?"

"My name is Liam." Killian insists, "I am no royalty."

"Ah, but your stance begs to differ; you do not hold yourself like a commoner. No matter how you slouch, you are regal."

Without warning, Killian's hood is gone from his head. "Ha! I knew it! You **are **Prince Killian!" The captain was absolutely gleeful. "Oh! My apologies your highness, it would seem I've forgotten my manners. I am Captain E. Swan, of the royal navy." Swan added bowing, bright red out of embarrassment.

"Swan? E. Swan? I know someone named E. Swan. Although, her name was Emma." Killian responded. Panic flashed across Swan's face as the flush drained away, leaving the captain looking pale as a ghost.


	2. Chapter 2

**The Runaway Swan**

**Chapter 2**

_Author's note: Captain Swan AU where Emma is a naval officer and Killian is prince and son of Snow and Charmin. Sorry Chapter 1 was so short, just building a background for the story. This one is another shortie, hope you like it :)_

She knew one day her lies would get her into trouble. She had no idea it would be like this.

It began when she was fifteen; she was the adopted daughter of a minor royal in the "Charming" kingdom. Her parents were unable to have a child of their own, so she was adopted at age eight. She was to be sent away at fifteen, after her parents "miraculously" became pregnant.

Not wishing to rejoin the foster system, Emma ran away, shaved her head, lied about her age, and joined the royal navy. Emma slowly climbed the ranks, forgetting her troubled past, becoming the perfect naval officer. If she was ever discovered to be female, she would be executed. Though, as Emma grew into her new persona, the idea of getting caught faded from her mind.

Then, one day, her past finds her again. There she is, standing in front of her childhood friend, Prince Killian; and he's talking to her, **about** her, he just doesn't know it yet. "Emma and I were best friends when we were little, but one day she just ran away. There's been no trace of her since."Killian continues with a sad smile, completely unaware of Emma's inner turmoil.

The guilt overwhelming Emma is what causes her to break and say, "Killian, it's me. I was about to be sent away anyways, back into the foster system. Running away made it my choice; I thought it would be better if I left because I wanted to, not because I was unwanted." Killian's facial expressions are comical to the point that Emma can't help but laugh, his eyes are practically popping out of his head, and his jaw is slack. Emma curtsies and says, "Surprise?"

"What- how- why- why didn't you tell me Swan?" Killian finally asks, "I- uh, we were devastated Emma!"

"I was going to leave a letter, but I couldn't risk someone finding out my secret." Emma pleads, "You can't tell anyone! They'll have my head for this!"


	3. Chapter 3

**The Runaway Swan**

**Chapter 3**

_Author's note: Captain Swan AU where Emma is a naval officer and Killian is prince and son of Snow and Charming. I'm still just building the plotline for the story. Sorry this took so long; I ended up rewriting it like ten times. Thank you for the likes, follows, and reviews; they mean a lot. Hope you like it :)_

Six years… it had been six years since Killian had last seen his best, and often only friend. After she ran away, he had assumed she was dead. Yet here she was, standing in front of him, her secret stuck in the uncomfortable space between them. Killian is stunned by the turn of events, but he quickly adopts a more formal façade, masking his inner pain and confusion.

"Well it wouldn't be a first." Killian's words cut through the tension, sharp and angry, "I thought you were dead Swan, we all did. No matter, I will do my part in preventing that from _actually _happening; I will keep your secret."

"I couldn't risk contact with you Killian. I could have been caught and executed at any moment."

"You must be joking lass; I've seen you many times while inspecting the naval ships, none the wiser about your identity. You could have approached me!"

"Ah yes, a lowly deckhand approaching the prince. That wouldn't have been suspicious at all." Emma's voice was practically dripping with sarcasm. "By the time I made it up to a decent rank, I was lost to my new persona. I'm sorry Jones, I was blocking out my past, and you ended up getting the worst from it."

His childhood nickname slipped from Emma's lips without her noticing, but Killian's breath hitches when he hears it. A wave of memories overwhelms Killian. The pair had been inseparable from the moment they first met. They were eight, and her family was visiting for some "adult" reason. Killian remembered it well; she came running into the Great Hall in a frilly pink dress that she looked extremely unhappy to be in.

"Hi! I'm Princess Emma!" she called, and curtseyed to the king and queen. Then, she turned to Killian and hugged him. "You must be Prince Killian! My parents told me about you! C'mon, let's go play!" Killian looked to his parents hesitantly and they nodded their approval.

"So I thought Killian was kind of long, and it doesn't really shorten well, so I've been trying to think of a name to call you." Emma rambled as she dragged Killian through the palace. "But, I figured you should have some say in this. If you had to create a whole new name for yourself, what would it be?" Killian stops suddenly. This hyper little girl, a total stranger at the time, managed to find his favorite part of the palace, the small garden that led down to the lake.

"How did you-?" He starts.

"How did I find my way here? Simple, I have this thing about water. But you didn't answer my question." Emma interrupts, still pulling Killian until they're at the water's edge.

"Um… I'll go with Jones, Liam Jones." Killian replied, amazed by the girl standing next to him.

"Jones it is!" Emma squealed with delight. "I think I'd keep Emma as my first name, but Nolan is _so _boring. I'd be Emma… Swan." She pointed out across the lake.

The memory stops abruptly, unfinished, as Killian snaps back to reality. He pulls Emma in for a tight hug.

"Oh how I've missed you Swan." He whispers, kissing the top of her head.

"Though I must say, this uniform suits you much better than those dresses you were forced to wear when we were younger." He adds, holding her away, and inspecting her attire.

"Now, I really must take my leave captain." Killian says with a teasing bow, "I hope to see you again soon." He pulls his hood back up and climbs onto his horse. As he rides away, Killian is amazed to discover how quickly Emma Swan could capture his heart. He was falling fast, and there was no going back now.


	4. Chapter 4

**The Runaway Swan**

**Chapter 4**

_Author's note: Captain Swan AU where Emma is a naval officer and Killian is prince and son of Snow and Charming. I'm sorry my chapters are so short, but I'm trying to do this from both Emma's and Killian's perspectives, but I find it weird to switch mid-chapter. This one is a bit longer. Thank you for the likes, follows, and reviews; they mean a lot. Hope you like it :)_

Emma stared after Killian as he rode away, a soft smile curving her lips. She was so glad he finally knew her secret, there had been many times she wanted to let him back into her life but was afraid the rest would come back too. Emma shakes her head and recomposes herself. Then she returns to the tavern to collect her men and prepare them for the next day.

-/-

The waves crash against the side of the ship on the morning light as the bandit queen, shepherd king, and their rebellious son board The Jewel.

"Good morning, your majesties." Emma bowed, "I would like you to meet my first lieutenant, Neal. He will be your guide this morning. If there are any questions or concerns that he is unsure about, I will be in my quarters, setting the itinerary for our next expedition."

"Thank you, captain." The king says, "However, I would ask that you take Prince Killian with you, he still hasn't learned proper attitude, maybe being near such an outstanding officer will help him. Besides, we feel it best that he stay out of official business until he learns his place." King David slips the captain a roll of parchment with the crew's new mission on it.

"Ah- Most certainly, your majesty." Emma says, momentarily taken aback by the blatant honesty of the king. Swan bows again, and leads the prince below deck to the captain's quarter.

"Wow, what a surprise to see you here." Killian jokes, launching himself onto Emma's bed, "Come join me, we can use this time to catch up." Killian pats the bed next to him. Emma ignores him and sits down at her desk. She pulls out the paper the king gave her and spreads it out in front of her when Killian rolls out of the bed, and plants himself on Emma's desk, right in the middle of her work.

"Your highness, please remove yourself from my desk, I have work to do."

"Oy, when did you become a stick in the mud? What happened to last night? Or are you just going to pretend nothing has changed?" Killian was now leaning into Emma's face, his joking attitude gone.

"No Killian, I'm not going to pretend anymore with you. I know there's no going back now. However, I need to keep up appearances. So if you don't mind, move your arse off my desk, now." Killian reluctantly got up from the desk and plopped himself back onto the bed.

"So where is your next adventure going to be, Captain Swan?" Killian teases.

"Oh, probably just another mission to check on our allies…" Emma attempts to maintain a straight face, but her eyes widen as she stares down at her next assignment. Killian notices the change, and starts to get up when Emma quickly folds the paper and tucks it into her pocket.

"Swan," Killian says, worry creeping into his voice. "Emma, look at me. What's wrong?"

"Nothing!" Emma replies a bit too quickly, "I believe your parents should be done soon, we should be on deck to see them, and you of course, off." Killian gives her a look but says no more on the subject, lingering in the room for a moment before following the captain above deck.

-/-

Emma re-enters the captain's quarters after bidding farewell to the visiting royalty. She sits down at her desk intending to look over the paper again and make plans, but before she can she notices a cream colored envelope sitting in the middle of her desk that wasn't there before.

"Killian." she growls, fingering at the wax seal on the envelope. Rolling her eyes, Emma popped the seal, and slid the card out of the envelope. It was an invitation to the King and Queen's masquerade ball. The note tucked in with the invitation read: _Please save me from tonight's torture, don't make me go through this alone. –Jones _with the addresses of a wigmaker and a dressmaker written below the signature.

She tucks the note and invitation into her pocket and pulls out the paper with the mission on it, determined to figure the mission out **before **getting distracted by Killian.

-/-

"First Lieutenant!" the captain called out as she emerged from her quarters, "I need you to assemble the entire crew on deck, fast as you can." Neal nods and rushes off to spread the word, amassing the ranks at an incredible speed.

"Good morning crew, since you're all probably wondering why I gathered you, I'll cut to the chase. The king has assigned us a task like no other we have faced in the past. Gentlemen, I suggest you spend this weekend with your families, for it may be the last time you ever see them. Come Monday, we leave for Wonderland. At sunrise, our means for transportation to and from that forsaken land will be delivered. I expect you all back and prepared by then. You are dismissed." Emma turns from her now thoroughly frightened crew to Neal.

"See that the ship is well stocked by Monday morning." We have a long journey ahead of us." With that, Emma walks of the ship reaching into her pocket for the note from Killian. Emma decides that it is necessary to stop by a small clothing store to purchase a disguise for the remainder of the afternoon, which she will spend shopping for her ball attire.

A short while later, Emma ducks into a thicket of trees, dress in hand. She quickly removes her uniform and pulls the simple dress on. Not knowing what to do, Emma tucks her uniform into the waterproof pouch she brought, and hides it under a pile of rocks. Swan fixes her hair for a moment, thankful she had neglected cutting it for a while, and sets off to find the wigmaker.

-/-

Emma walks toward the palace doors, invitation in hand. She was utterly unrecognizable with a long brown wig styled into an intricate and elegant up-do, with a delicate tiara perched on top. Her mask was a pale blue that matched her dress perfectly. The dress was one fit for a swan princess, with feathers accenting the sleeves.

She passed her card to the guard at the entrance and made her way inside, where she was stopped by King David.

"I am King David, who do I have the honor to welcome into my home?"

"I'm Princess EmMilah, Princess Milah." Emma replied in her natural voice, one much higher than she was accustomed to using on the Jewel, curtseying to the king.

"It is a pleasure to have you here." David responded.

Emma wandered through the crowd, searching for the familiar head of always-messy, black hair. Not looking where she's going, Emma runs straight into someone.

"Oh! I'm so sorry! I'm Prince Killian." He says, extending his hand.

"Princess Milah." Emma lies smoothly, placing her hand in his. He pulls her hand up and lightly kisses it.

"Allow me to make up for my earlier clumsiness with a dance, princess?" Killian asks, not releasing Emma's hand.

"You can have one, wouldn't want to tempt your clumsy side for too long." Emma jokes, following him towards the center of the dance floor.

"Pardon me for asking, princess, but have we met before? Your eyes seem familiar."

"Maybe, but I doubt I'd ever forget meeting you." She replies as they are swept away into the movements of the other dancers.

"One dance" she had said, but one dance turned into many, many more. Everyone in the room was staring at the duo that were so lost in each other, they didn't even notice the time passing.

The clock tolls midnight, which causes Emma to snap out of her Killian-induced trance. She drags him through the crowd, away from all the staring.

"That was…" Killian begins breathlessly.

"A one time thing." Emma cuts him off and turns to leave.

"Wait!" He calls, grabbing Emma's arm, "Can I know your last name, Milah?" She turns back to face him and leans in close.

"Swan." She whispers, lips brushing his ear, before pulling away and hastily exiting the ballroom. Killian makes a move to follow her, when his mother drags him out onto the dance floor.

"So, who was that?" Snow asks.

"I have no idea." Killian replies honestly, still in shock from his encounter with the entrancing princess.

-/-

The "princess" on the other hand, was currently digging through her third pile of rocks, desperate to find her naval uniform.

"It's a good thing I dismissed everybody this afternoon." Emma mutters, trudging back to the ship in her gown and wig. Once onboard, Swan dashes to her quarter, slamming the door shut and locking it behind her. She's almost certain no one saw her, but she quickly rids herself of any trace of femininity, pulling her pajamas on. She locks her wig, tiara, mask, dress, and shoes in the trunk in her room where she stores the money she took from her former parents. Swan walks over to her bed, lies down, and quickly falls asleep.

-/-

After a weekend of barking orders at lazy and clumsy deck hands, Monday morning the Jewel and her crew are ready to go, except for the magic beans needed to cross realms. As the sun begins rising off the starboard side, a young major boards the ship, walking straight for Captain Swan.

"Sir, your beans. One will be used to open a portal leaving this land, the other to return. Guard it with your life. Also, I have a notice here for you; you seem to have a new recruit. He should already be among your ranks."

Emma salutes and the man departs. She unrolls the small scroll and her eyes practically pop out when she sees the name inscribed on the parchment. _Liam Jones._


End file.
